Code accompanying Gardner et. al. (2019)
For the processed pseudogene discovery pipeline included in the manuscript, please see this git repo.
This repo will reproduce all the figures and supplemental data included in the paper which were derived from R. Some statistical tests and tabulated numbers are also included.
While there is no Figure3.Rmd file as Figure3 was derived from omics data and/or PCR and thus does not include any statistical analysis, raw blots included in this figure are provided in the folder Figures/Figure3/RawBlots.
This repo is an Rstudio markdown notebook. For more information on how to use R-markdown please see this link. To use this repo, simply:
git clone https://github.com/eugenegardner/MEIPaper.git
cd MEIPaper/
tar -zxvf ./Figures/Supplement/RawData/genodepth.di.tar.gz
tar -zxvf ./Figures/Supplement/RawData/GTEx.expr.tar.gz
tar -zxvf ./Figures/Figure1/RawData/SNV.frq.tar.gz
And load the included MEIPaper.Rproj file in the top-level directory into Rstudio via File -> Open Project.
You can then open the individual *.Rmd notebooks in each of the individual "Figure" folders.
For any questions please open a new github issue.
Gardner et. al., Contribution of Retrotransposition to Developmental Disorders, Nature Communications, 2019